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vahidAK / NanoMethPhase

Methylation Phasing for Nanopore Sequencing
GNU General Public License v3.0
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Does NanoMethPhase support Clair3? #3

Closed PanZiwei closed 3 years ago

PanZiwei commented 3 years ago

Hi, I noticed that Clair3 (https://github.com/HKU-BAL/Clair3) is released recently. Does NanoMethPhase is compatible with the latest Clair? Or it should stick to Clair2 for reproduction?

vahidAK commented 3 years ago

Hi @PanZiwei ,

Yes, it does not matter which variant caller you are using. You can use any variant caller and your variants can come from any source. As NanoMethPhase requires the vcf file to be phased, the thing that matters is that the output of your phased vcf file is compatible with the tool (discussed in issue #1). So, it also does not matter which tool you are using afterwards to phase the variants as long as the format is correct (in our work we used WhatsHap and it works very well. So if you use whatshap the vcf is already in the format required by NanoMethPhase).

BTW, I have recently added an image to the readme file that represents a nice visualization workflow of the steps that need to be done to get phased methylome.

Let me know if you had any questions, Vahid

PanZiwei commented 3 years ago

If I understand it correctly, the variant caller is no longer in need if I directly use Clair inside the NanoMethPhase docker image, right? It seems that it takes an extremely long time to build the docker image via singularity, have you encountered the problem before? Also, NanoMethPhase is able to call allele-specific methylation if I follow the workflow correctly? Thank you in advance for your reply!

vahidAK commented 3 years ago

You can use your local installed version of Clair or any variant caller. No need to use Clair installed along NanoMethPhase. For singularity, my colleague, @garantjm, can help you.

Yes, If you follow the workflow you will have allele-specific methylation along with several other useful outputs.

Vahid

PanZiwei commented 3 years ago

Thank you so much for your quick response.

I will first have a try on the docker image for convenience. I have already submitted the job and will keep you posted if the image failed to build overnight.

PanZiwei commented 3 years ago

I successfully install it via the singularity.